RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

Abstract Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific...

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Autores principales:	Karim Sorkheh, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, Júlia Halász
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4507f04f66644d77ac5e5516ec8e856c
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spelling	oai:doaj.org-article:4507f04f66644d77ac5e5516ec8e856c2021-12-02T16:06:45ZRETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species10.1038/s41598-017-06084-42045-2322https://doaj.org/article/4507f04f66644d77ac5e5516ec8e856c2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06084-4https://doaj.org/toc/2045-2322Abstract Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.Karim SorkhehMehrana Koohi DehkordiSezai ErcisliAttila HegedusJúlia HalászNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-17 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Karim Sorkheh Mehrana Koohi Dehkordi Sezai Ercisli Attila Hegedus Júlia Halász RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
description	Abstract Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
format	article
author	Karim Sorkheh Mehrana Koohi Dehkordi Sezai Ercisli Attila Hegedus Júlia Halász
author_facet	Karim Sorkheh Mehrana Koohi Dehkordi Sezai Ercisli Attila Hegedus Júlia Halász
author_sort	Karim Sorkheh
title	RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_short	RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_full	RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_fullStr	RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_full_unstemmed	RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_sort	retracted article: comparison of traditional and new generation dna markers declares high genetic diversity and differentiated population structure of wild almond species
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/4507f04f66644d77ac5e5516ec8e856c
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RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

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